drl,

That's odd. I got the expected result when I ran your whole script. However when I ran each step of the script, join still did not work. Here is what I did:

$ cat data1
rs10051507 5 q21.3
rs10051514 5 p15.32
rs10051527 5 q21.2
rs1005152 7 q21.3
rs10051540 5 q21.3
rs10051548 5 q21.1
rs1005155 X q27.3
rs10051594 5 q34

$ cat data2
rs1003456 3
rs1005152 3

$ sort data1 >t1

$ sort data2>t2

$ join t1 t2

Why is that?